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1.
BMC Bioinformatics ; 22(1): 4, 2021 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-33407073

RESUMEN

BACKGROUND: Statistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein-protein interaction (PPI) structures. In previous works we decomposed the statistical potentials in different terms, named Split-Statistical Potentials, accounting for the type of amino acid pairs, their hydrophobicity, solvent accessibility and type of secondary structure. These potentials have been successfully used to identify near-native structures in protein structure prediction, rank protein docking poses, and predict PPI binding affinities. RESULTS: Here, we present the SPServer, a web server that applies the Split-Statistical Potentials to analyze protein folds and protein interfaces. SPServer provides global scores as well as residue/residue-pair profiles presented as score plots and maps. This level of detail allows users to: (1) identify potentially problematic regions on protein structures; (2) identify disrupting amino acid pairs in protein interfaces; and (3) compare and analyze the quality of tertiary and quaternary structural models. CONCLUSIONS: While there are many web servers that provide scoring functions to assess the quality of either protein folds or PPI structures, SPServer integrates both aspects in a unique easy-to-use web server. Moreover, the server permits to locally assess the quality of the structures and interfaces at a residue level and provides tools to compare the local assessment between structures. SERVER ADDRESS: https://sbi.upf.edu/spserver/ .


Asunto(s)
Mapas de Interacción de Proteínas/fisiología , Estructura Secundaria de Proteína , Proteínas , Programas Informáticos , Aminoácidos/química , Aminoácidos/metabolismo , Internet , Bases del Conocimiento , Modelos Estadísticos , Proteínas/química , Proteínas/metabolismo
2.
BMC Bioinformatics ; 22(1): 8, 2021 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-33407077

RESUMEN

BACKGROUND: Protein inter-residue contact and distance prediction are two key intermediate steps essential to accurate protein structure prediction. Distance prediction comes in two forms: real-valued distances and 'binned' distograms, which are a more finely grained variant of the binary contact prediction problem. The latter has been introduced as a new challenge in the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14) 2020 experiment. Despite the recent proliferation of methods for predicting distances, few methods exist for evaluating these predictions. Currently only numerical metrics, which evaluate the entire prediction at once, are used. These give no insight into the structural details of a prediction. For this reason, new methods and tools are needed. RESULTS: We have developed a web server for evaluating predicted inter-residue distances. Our server, DISTEVAL, accepts predicted contacts, distances, and a true structure as optional inputs to generate informative heatmaps, chord diagrams, and 3D models. All of these outputs facilitate visual and qualitative assessment. The server also evaluates predictions using other metrics such as mean absolute error, root mean squared error, and contact precision. CONCLUSIONS: The visualizations generated by DISTEVAL complement each other and collectively serve as a powerful tool for both quantitative and qualitative assessments of predicted contacts and distances, even in the absence of a true 3D structure.


Asunto(s)
Biología Computacional/métodos , Internet , Modelos Moleculares , Proteínas , Aminoácidos/química , Aminoácidos/metabolismo , Conformación Proteica , Proteínas/química , Proteínas/metabolismo
3.
Food Chem ; 343: 128397, 2021 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-33406569

RESUMEN

Chocolate is an important source of free bioactive amines and amino acids which play important roles in human health. Considering the limited information on the bioaccessibility of these compounds from chocolate, the objective of this study was to characterize their profiles and bioaccessibility in 70% cocoa dark chocolate through in vitro simulation of oral, gastric and intestinal digestions. Seven amines were detected; polyamines were predominant before in vitro digestion, whereas tyramine, cadaverine and spermidine after digestion. All amines showed high bioaccessibility with slight influence of digestive enzymes. Amines increased after gastrointestinal digestion: tyramine (13-fold), tryptamine (9-fold), others (2.4-4.2-fold) and histamine appeared. All amino acids, GABA and ammonia were detected in chocolate, and their contents increased after in vitro digestion due to digestive enzymes (4.6, 2.8 and 2.1, respectively). Dark chocolate protein is a good source of tryptophan, phenylalanine + tyrosine, isoleucine, histidine, but limiting for lysine, leucine, and threonine.


Asunto(s)
Aminas/metabolismo , Aminoácidos/metabolismo , Cacao/metabolismo , Chocolate/análisis , Aminas/análisis , Aminoácidos/análisis , Amoníaco/metabolismo , Cacao/química , Cromatografía Líquida de Alta Presión , Análisis por Conglomerados , Histamina/análisis , Histamina/metabolismo , Humanos , Valor Nutritivo , Poliaminas/análisis , Poliaminas/metabolismo , Análisis de Componente Principal , Ácido gamma-Aminobutírico/análisis
4.
Nat Commun ; 12(1): 562, 2021 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-33495467

RESUMEN

Cell adhesion has tremendous impact on the function of culture platforms and implants. Cell-adhesive proteins and peptides have been extensively used for decades to promote cell adhesion, however, their application suffers from their easy enzymatic degradation, difficulty in large-scale preparation and expensiveness. To develop the next-generation cell-adhesive materials, we mimic the cell adhesion functions and mechanisms of RGD and KRSR peptides and design cell-adhesive cationic-hydrophobic amphiphilic ß-amino acid polymers that are stable upon proteolysis and easily prepared in large scale at low cost. The optimal polymer strongly promotes cell adhesion, using preosteoblast cell as a model, by following dual mechanisms that are independent of sequence and chirality of the statistic copolymer. Our strategy opens avenues in designing the next-generation cell-adhesive materials and may guide future studies and applications.


Asunto(s)
Aminoácidos/metabolismo , Oligopéptidos/metabolismo , Polímeros/metabolismo , Secuencia de Aminoácidos , Aminoácidos/química , Animales , Adhesión Celular/efectos de los fármacos , Adhesión Celular/fisiología , Línea Celular , Medio de Cultivo Libre de Suero/farmacología , Hidrogeles/química , Hidrogeles/metabolismo , Ratones , Oligopéptidos/química , Osteoblastos/citología , Osteoblastos/efectos de los fármacos , Osteoblastos/metabolismo , Espectroscopía de Fotoelectrones , Polietilenglicoles/química , Polietilenglicoles/metabolismo , Polímeros/química , Propiedades de Superficie
5.
Life Sci ; 269: 119046, 2021 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-33453245

RESUMEN

BACKGROUND: The pandemic of the coronavirus disease 2019 (COVID-19) has brought a global public health crisis. However, the pathogenesis underlying COVID-19 are barely understood. METHODS: In this study, we performed proteomic analyses of airway mucus obtained by bronchoscopy from severe COVID-19 patients. In total, 2351 and 2073 proteins were identified and quantified in COVID-19 patients and healthy controls, respectively. RESULTS: Among them, 92 differentiated expressed proteins (DEPs) (46 up-regulated and 46 down-regulated) were found with a fold change >1.5 or <0.67 and a p-value <0.05, and 375 proteins were uniquely present in airway mucus from COVID-19 patients. Pathway and network enrichment analyses revealed that the 92 DEPs were mostly associated with metabolic, complement and coagulation cascades, lysosome, and cholesterol metabolism pathways, and the 375 COVID-19 only proteins were mainly enriched in amino acid degradation (Valine, Leucine and Isoleucine degradation), amino acid metabolism (beta-Alanine, Tryptophan, Cysteine and Methionine metabolism), oxidative phosphorylation, phagosome, and cholesterol metabolism pathways. CONCLUSIONS: This study aims to provide fundamental data for elucidating proteomic changes of COVID-19, which may implicate further investigation of molecular targets directing at specific therapy.


Asunto(s)
Aminoácidos/metabolismo , Moco/virología , Proteínas/metabolismo , Anciano , Broncoscopía , Estudios de Casos y Controles , Colesterol/metabolismo , Enfermedad Crítica , Femenino , Humanos , Masculino , Persona de Mediana Edad , Proteómica , Índice de Severidad de la Enfermedad
6.
Ecotoxicol Environ Saf ; 211: 111921, 2021 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-33486382

RESUMEN

Citric acid (CA) can regulate the balance of anions and cations in plants, and improve their resistance to heavy metals. It is not clear if foliar application with CA has any effect on migration of Cd and Mn in rice plant. In this work, a low-Cd-accumulating indica rice line (P7) and a high-Cd-accumulating line (HZ) were used to investigate the influence of CA on the transport of Cd and Mn as well as amino acid metabolism in grains. Content of Cd in grains and other organs increased with the increase of Cd content (0.1-2.4 mg kg-1) in soil, while decreased with the foliar application with CA. With the increase of Cd content in rice grains, the content of most amino acids in HZ, P7, HZ+CA and P7 + CA showed an obvious decline trend. Foliar application with CA efficiently raised the Mn:Cd ratio in grains and nodes of both HZ and P7. Meanwhile, the expression levels of OsNramp2, 3 and 5 in panicles were efficiently enhanced by CA application when plants grew in soil with Cd content of 0.6-2.4 mg kg-1. The increasing effect of CA on the content of 4 amino acids (i.e., Glu, Phe, Thr and Ala) in grains was related to varieties and Cd pollution. These results indicate that foliar application with CA can regulate the transport of Cd and Mn in the opposite directions in tissues and inhibit Cd accumulation in grains by enhancing expression of OsNRAMP 2, 3 or 5 and triggering the defense response of some amino acids in Cd-contaminated environment.


Asunto(s)
Aminoácidos/metabolismo , Cadmio/metabolismo , Ácido Cítrico/farmacología , Grano Comestible/fisiología , Manganeso/metabolismo , Sustancias Protectoras/farmacología , Transporte Biológico , Contaminación Ambiental , Metales Pesados/análisis , Oryza/metabolismo , Hojas de la Planta/metabolismo , Raíces de Plantas/metabolismo , Suelo/química , Contaminantes del Suelo/análisis
7.
J Anim Sci ; 99(1)2021 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-33515467

RESUMEN

Energy values and amino acid (AA) digestibility of dried yeast (DY) and soybean meal (SBM) were determined in 2 experiments with growing pigs. Experiment 1 was conducted to determine the digestible energy (DE) and metabolizable energy (ME) in DY and SBM. Thirty barrows with a mean initial body weight (BW) of 20.6 kg (SD = 1.04) were assigned to 5 dietary treatments in a randomized complete block design with period and BW as blocking factors. A reference diet was prepared with corn, canola meal, and soybean oil as energy-contributing ingredients. Four additional diets were prepared by adding 5% and 10% DY or SBM at the expense of energy-contributing ingredients in the reference diet. The ratio of corn, canola meal, and soybean oil was kept consistent across the experimental diets. Each experimental period consisted of 5-d adaptation and 5-d quantitative collection of feces and urine. Test ingredient-associated DE or ME intake (kcal/d) was regressed against test ingredient intake [kg dry matter (DM)/d] to estimate the DE or ME in test ingredients as the slope of linear regression model. The DE in DY was estimated at 3,933 kcal/kg DM, which was not different from the estimated DE in SBM at 4,020 kcal/kg DM. Similarly, there was no difference between DY and SBM in the estimated ME (3,431 and 3,756 kcal/kg DM, respectively). Experiment 2 was conducted to determine the standardized ileal digestibility (SID) of AA in DY and SBM. Twenty-one barrows with a mean initial BW of 20.0 kg (SD = 1.31) were surgically fitted with T-cannulas at the distal ileum and assigned to 3 dietary treatments in a randomized complete block design with BW as a blocking factor. Two semi-purified diets containing DY or SBM as the sole nitrogen source and one nitrogen-free diet (NFD) were prepared. The NFD was used to estimate the basal ileal endogenous losses of CP and AA. Pigs were fed the 3 diets for 5 d as adaptation, followed by 2 d of feeding with ileal digesta collection. The SID of AA, except Gly and Pro, in DY was less (P < 0.05) than in SBM. The SID of indispensable AA in DY ranged from 64.1% for Thr to 85.2% for Arg, and those in SBM ranged from 83.9% for Thr to 91.8% for Arg. In conclusion, energy values of DY are not different from those of SBM, whereas AA in DY is less digestible than in SBM. The estimated DE and ME as well as the SID of AA in DY and SBM can be used in diet formulation for growing pigs using these ingredients.


Asunto(s)
Soja , Levadura Seca , Aminoácidos/metabolismo , Alimentación Animal/análisis , Fenómenos Fisiológicos Nutricionales de los Animales , Animales , Dieta/veterinaria , Digestión , Metabolismo Energético , Íleon/metabolismo , Soja/metabolismo , Porcinos
8.
Nat Commun ; 12(1): 328, 2021 01 12.
Artículo en Inglés | MEDLINE | ID: mdl-33436566

RESUMEN

While genome recoding using quadruplet codons to incorporate non-proteinogenic amino acids is attractive for biotechnology and bioengineering purposes, the mechanism through which such codons are translated is poorly understood. Here we investigate translation of quadruplet codons by a +1-frameshifting tRNA, SufB2, that contains an extra nucleotide in its anticodon loop. Natural post-transcriptional modification of SufB2 in cells prevents it from frameshifting using a quadruplet-pairing mechanism such that it preferentially employs a triplet-slippage mechanism. We show that SufB2 uses triplet anticodon-codon pairing in the 0-frame to initially decode the quadruplet codon, but subsequently shifts to the +1-frame during tRNA-mRNA translocation. SufB2 frameshifting involves perturbation of an essential ribosome conformational change that facilitates tRNA-mRNA movements at a late stage of the translocation reaction. Our results provide a molecular mechanism for SufB2-induced +1 frameshifting and suggest that engineering of a specific ribosome conformational change can improve the efficiency of genome recoding.


Asunto(s)
Sistema de Lectura Ribosómico/genética , Genoma Bacteriano , ARN de Transferencia/genética , Salmonella typhimurium/genética , Aminoácidos/metabolismo , Aminoacilación , Anticodón/genética , Proteínas Bacterianas/metabolismo , Secuencia de Bases , Codón/genética , Escherichia coli/metabolismo , Transferencia Resonante de Energía de Fluorescencia , Guanosina Trifosfato/metabolismo , Hidrólisis , Metilación , Modelos Moleculares , Conformación de Ácido Nucleico , Motivos de Nucleótidos/genética , ARN de Transferencia/química , ARN de Transferencia/metabolismo , Ribosomas/metabolismo
9.
Nat Commun ; 12(1): 676, 2021 01 29.
Artículo en Inglés | MEDLINE | ID: mdl-33514729

RESUMEN

Across the evolutionary history of insects, the shift from nitrogen-rich carnivore/omnivore diets to nitrogen-poor herbivorous diets was made possible through symbiosis with microbes. The herbivorous turtle ants Cephalotes possess a conserved gut microbiome which enriches the nutrient composition by recycling nitrogen-rich metabolic waste to increase the production of amino acids. This enrichment is assumed to benefit the host, but we do not know to what extent. To gain insights into nitrogen assimilation in the ant cuticle we use gut bacterial manipulation, 15N isotopic enrichment, isotope-ratio mass spectrometry, and 15N nuclear magnetic resonance spectroscopy to demonstrate that gut bacteria contribute to the formation of proteins, catecholamine cross-linkers, and chitin in the cuticle. This study identifies the cuticular components which are nitrogen-enriched by gut bacteria, highlighting the role of symbionts in insect evolution, and provides a framework for understanding the nitrogen flow from nutrients through bacteria into the insect cuticle.


Asunto(s)
Exoesqueleto/crecimiento & desarrollo , Hormigas/crecimiento & desarrollo , Microbioma Gastrointestinal/fisiología , Herbivoria/fisiología , Simbiosis/fisiología , Aminoácidos/metabolismo , Animales , Hormigas/metabolismo , Hormigas/microbiología , Quitina/biosíntesis , Proteínas de Insectos/biosíntesis , Nitrógeno/metabolismo
10.
Nat Metab ; 3(1): 43-58, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33432202

RESUMEN

The mammalian liver is a central hub for systemic metabolic homeostasis. Liver tissue is spatially structured, with hepatocytes operating in repeating lobules, and sub-lobule zones performing distinct functions. The liver is also subject to extensive temporal regulation, orchestrated by the interplay of the circadian clock, systemic signals and feeding rhythms. However, liver zonation has previously been analysed as a static phenomenon, and liver chronobiology has been analysed at tissue-level resolution. Here, we use single-cell RNA-seq to investigate the interplay between gene regulation in space and time. Using mixed-effect models of messenger RNA expression and smFISH validations, we find that many genes in the liver are both zonated and rhythmic, and most of them show multiplicative space-time effects. Such dually regulated genes cover not only key hepatic functions such as lipid, carbohydrate and amino acid metabolism, but also previously unassociated processes involving protein chaperones. Our data also suggest that rhythmic and localized expression of Wnt targets could be explained by rhythmically expressed Wnt ligands from non-parenchymal cells near the central vein. Core circadian clock genes are expressed in a non-zonated manner, indicating that the liver clock is robust to zonation. Together, our scRNA-seq analysis reveals how liver function is compartmentalized spatio-temporally at the sub-lobular scale.


Asunto(s)
Relojes Circadianos/genética , Expresión Génica/fisiología , Hígado/metabolismo , Periodicidad , Algoritmos , Aminoácidos/metabolismo , Animales , Metabolismo de los Hidratos de Carbono/genética , Perfilación de la Expresión Génica , Hepatocitos/metabolismo , Metabolismo de los Lípidos/genética , Masculino , Ratones , Ratones Endogámicos C57BL , Chaperonas Moleculares/metabolismo , Proteínas Circadianas Period/genética , ARN Mensajero/biosíntesis , ARN Mensajero/genética , Vía de Señalización Wnt/genética
11.
Ecotoxicol Environ Saf ; 207: 111281, 2021 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-32919195

RESUMEN

Epidemiological studies of human and animal experiments indicated that gestational exposure to atmospheric pollutants could be followed by the abnormal placental development. However, the effects of this exposure on the placental transportation for nutrients have not been systematically investigated. In this study, fine particulate matters (PM2.5) samples were collected in Taiyuan and pregnant rodent models were administered with 3 mg/kg b.w. PM2.5 by oropharyngeal aspiration every other day starting on embryonic day 0.5 (E0.5). Then the pregnant mice were sacrificed and their placentas were collected at different time points. The results showed that maternal PM2.5 exposure (MPE) disrupted the expression of proliferating cell nuclear antigen (PCNA) at all time points and inhibited the cell proliferation in placenta. Following that, the capacity for placental nutrient transport was impaired. The changes at E18.5 were observed most significantly, showing the altered mRNA expression of amino acid, long-chain polyunsaturated fatty acid (LCPUFA), glucose and folate transporters. In addition, the glycogen content was elevated at E18.5, and the triglyceride content was increased at E13.5 and E15.5 and decreased at E18.5 in the placenta after MPE. In a word, the adverse effect induced by MPE revealed that MPE led tothe disruption on the nutrient supply to the developing fetus via modulating the abundance of placental nutrient transporters (PNT).


Asunto(s)
Contaminantes Atmosféricos/toxicidad , Exposición Materna/efectos adversos , Nutrientes/metabolismo , Material Particulado/toxicidad , Placenta/efectos de los fármacos , Contaminantes Atmosféricos/metabolismo , Aminoácidos/metabolismo , Animales , Transporte Biológico , Proliferación Celular/efectos de los fármacos , Ácidos Grasos/metabolismo , Femenino , Glucosa/metabolismo , Glucógeno/metabolismo , Humanos , Intercambio Materno-Fetal/efectos de los fármacos , Ratones , Material Particulado/metabolismo , Placenta/metabolismo , Placenta/patología , Embarazo
12.
Food Chem ; 338: 128018, 2021 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-32932086

RESUMEN

The umami-enhancing effect of typical kokumi-active γ-glutamyl peptides was verified by sensory evaluation. To investigate the umami-enhancing molecular mechanism of the peptide on monosodium glutamate (MSG) taste, a novel hypothetical receptor, taste type 1 receptor 3 (T1R3)-MSG complex, was constructed. These peptides demonstrated strong interactions with T1R3-MSG. Moreover, four amino acid residues, Glu-301, Ala-302, Thr-305, and Ser-306, were critical in ligand-receptor interactions. In detail, γ-Glu-γ-Glu-Val (γ-E-γ-EV) readily interacts with T1R3 through hydrogen bonds and hydrophobic interactions. While γ-E-γ-EV did not bind to MSG, γ-Glu-Val (γ-EV) and γ-Glu-Leu (γ-EL) showed high binding affinity to MSG and interacted with T1R3 through hydrophobic bonds suggesting that the interactions between dipeptides and T1R3-MSG were weaker than tripeptides. These results demonstrated that kokumi-active γ-glutamyl peptides could enhance the umami taste of MSG, and exhibit synergistic effects in activating T1R3. This study provides a theoretical reference for interactions between the novel umami-enhancing substances and umami receptor.


Asunto(s)
Dipéptidos/metabolismo , Receptores Acoplados a Proteínas G/metabolismo , Glutamato de Sodio/metabolismo , Gusto , Adulto , Aminoácidos/química , Aminoácidos/metabolismo , Dipéptidos/química , Femenino , Aromatizantes/química , Aromatizantes/farmacología , Humanos , Enlace de Hidrógeno , Masculino , Persona de Mediana Edad , Modelos Moleculares , Simulación del Acoplamiento Molecular , Receptores Acoplados a Proteínas G/química , Glutamato de Sodio/química , Glutamato de Sodio/farmacología , Gusto/efectos de los fármacos
13.
Food Chem ; 338: 128020, 2021 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-32932087

RESUMEN

Plant-based protein foods are increasingly common, but data on their nutritional protein quality are scarce. This study evaluated it for seitan (wheat-based food), tofu (soya-based food), soya milk, and a pea emulsion. The true ileal digestibility (TID) of their amino acids was determined in minipigs, to calculate the digestible indispensable amino acid score (DIAAS). The TID of the proteins was high and not significantly different between the foods tested: 97% for seitan, 95% for tofu, 92% for soya milk and 94% for pea emulsion. There were only minor differences in individual amino acid TIDs. DIAAS ranking was thus essentially driven by the amino acid composition of the food: soya-based food > pea emulsion > seitan. Nevertheless, the lower TID of sulphur-containing amino acids in tofu than in soya milk induced a significant decrease in DIAAS (from 117% to 97%), highlighting the importance of the matrix effect on nutritional protein quality.


Asunto(s)
Aminoácidos/análisis , Proteínas en la Dieta/farmacocinética , Íleon/metabolismo , Proteínas de Plantas/farmacocinética , Aminoácidos/metabolismo , Aminoácidos Esenciales/análisis , Aminoácidos Esenciales/metabolismo , Animales , Digestión , Íleon/efectos de los fármacos , Valor Nutritivo , Proteínas de Plantas/metabolismo , Alimentos de Soja , Leche de Soja , Soja/química , Porcinos , Porcinos Enanos , Triticum/química
14.
Food Chem ; 338: 128126, 2021 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-33091993

RESUMEN

Tomato fruits contain much organic acids and γ-aminobutyric acid (GABA) during ripening which are beneficial to human health. The effects of 4 kJ/m2 UV-C treatment on the contents of organic acids and GABA, and the expression of related genes in tomato fruits during storage at 13 °C were investigated. The results showed that UV-C treatment significantly increased the organic acids and total soluble protein contents, whereas decreased the free amino acids and glutamate contents. Besides, UV-C treatment enhanced GAD activity while reduced GABA-T activity, which resulted in accumulation of GABA. Moreover, the genes involved in the biosynthesis of organic acids and GABA were up-regulated, including CS, PEPC1, PEPC2, mMDH, cMDH, GAD1, GAD2, and GAD3, while GABA-T1 and GABA-T3 which involved in GABA degradation were obviously decreased by UV-C treatment. These results indicated that UV-C treatment might be an effective approach to accumulate organic acids and GABA during tomato fruits ripening.


Asunto(s)
Almacenamiento de Alimentos , Frutas/metabolismo , Frutas/efectos de la radiación , Lycopersicon esculentum/metabolismo , Lycopersicon esculentum/efectos de la radiación , Rayos Ultravioleta , Ácido gamma-Aminobutírico/metabolismo , Aminoácidos/metabolismo , Glutamato Descarboxilasa/metabolismo , Ácido Glutámico/metabolismo
15.
Anal Chem ; 93(3): 1604-1611, 2021 01 26.
Artículo en Inglés | MEDLINE | ID: mdl-33356171

RESUMEN

Carboxylic metabolites are an important class of metabolites, which widely exist in mammals with various types. Chemical isotope labeling liquid chromatography-mass spectrometry (CIL-LC-MS) has been widely used for the detection of carboxylated metabolites. However, high coverage analysis of carboxylated metabolites in biological samples is still challenging due to improper reactivity and selectivity of labeling reagents to carboxylated metabolites. In this study, we used N-methylphenylethylamine (MPEA) to label various types of carboxylated metabolites including short-chain fatty acids (SCFAs), medium-chain fatty acids (MCFAs), long-chain fatty acids (LCFAs), polycarboxylic acids (polyCAs), amino acids (AAs), and aromatic acids. Additionally, metabolites containing other functional groups, such as phenol, sulfhydryl, and phosphate groups, could not be labeled under the conditions of MPEA labeling. After MPEA labeling, the detection sensitivity of carboxylic acids was increased by 1-2 orders of magnitude, and their chromatographic retention on a reversed-phase (RP) column was enhanced (RT > 3 min). Under optimized labeling conditions, we used MPEA and d3-N-methylphenylethylamine (d3-MPEA) for high coverage screening of carboxylated metabolites in HepG2 cells by ultrahigh-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS). As a result, a total of 403 potential carboxylated metabolites were obtained of which 68 were confirmed based on our established in-house chemically labeled metabolite database (CLMD). SCFAs, MCFAs, LCFAs, polyCAs, AAs, and aromatic acids were all detected in HepG2 cell extracts. Due to the successful identification of AAs, the current method increased the coverage of carboxylated metabolites compared with our previous work. Moreover, 133 and 109 carboxylated metabolites with changed contents were obtained in HepG2 cells incubated with curcumin and R-3-hydroxybutyric acid, respectively. In general, our established method realized high coverage analysis of carboxylated metabolites in HepG2 cells.


Asunto(s)
Aminoácidos/análisis , Ácidos Carboxílicos/análisis , Ácidos Grasos/análisis , Metanfetamina/análogos & derivados , Aminoácidos/metabolismo , Ácidos Carboxílicos/metabolismo , Cromatografía Líquida de Alta Presión , Ácidos Grasos/metabolismo , Células Hep G2 , Humanos , Espectrometría de Masas , Metanfetamina/química , Metanfetamina/metabolismo , Estructura Molecular
16.
Aquat Toxicol ; 231: 105715, 2021 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-33341507

RESUMEN

This study was conceptualized in order to assess the 96-h LC50 of bifenthrin (BF) in O. niloticus and also to measure the biochemical, behavioral, and molecular responses of the fish suchronically exposed to a sub-lethal concentration of the insecticide. The role of Petroselinum crispum essential oil (PEO) supplementation in mitigating the resulted neurotoxic insult was also investigated. The acute toxicity study revealed that the 96-h LC50 of BF is 6.81 µg/L, and varying degrees of behavioral changes were recorded in a dose-dependent manner. The subchronic study revealed reduction of dissolved oxygen and increased ammonia in aquaria of BF-exposed fish. Clinical signs revealed high degree of discomfort and aggressiveness together with reductions in survival rate and body weight gain. The levels of monoamines in brain, and GABA and amino acids in serum were reduced, together with decreased activities of Na+/K+-ATPase and acetylcholine esterases (AchE). The activities of antioxidant enzymes were also diminshed in the brain while oxdative damage and DNA breaks were elevated. Myeloperoxidase (MPO) activity in serum increased with overexpression of the pro-inflammatory cytokines in the brain tissue. BF also upregulated the expression of brain-stress related genes HSP70, Caspase-3 and P53. Supplemention of PEO to BF markedly abrogated the toxic impacts of the insecticide, specially at the high level. These findings demonstrate neuroprotective, antioxidant, genoprotective, anti-inflammatory and antiapoptic effects of PEO in BF-intoxicated fish. Based on these mechanistic insights of PEO, we recommend its use as an invaluable supplement in the fish feed.


Asunto(s)
Encéfalo/patología , Cíclidos/fisiología , Suplementos Dietéticos , Inflamación/patología , Aceites Volátiles/farmacología , Petroselinum/química , Piretrinas/toxicidad , Acetilcolinesterasa/metabolismo , Aminoácidos/metabolismo , Animales , Antioxidantes/metabolismo , Conducta Animal , Biomarcadores/metabolismo , Encéfalo/efectos de los fármacos , Cíclidos/crecimiento & desarrollo , Citocinas/metabolismo , Daño del ADN , Regulación de la Expresión Génica/efectos de los fármacos , Insecticidas/metabolismo , Dosificación Letal Mediana , Neurotoxinas/toxicidad , Neurotransmisores/metabolismo , Estrés Oxidativo/efectos de los fármacos , ATPasa Intercambiadora de Sodio-Potasio/metabolismo , Análisis de Supervivencia , Contaminantes Químicos del Agua/toxicidad , Calidad del Agua , Ácido gamma-Aminobutírico/metabolismo
17.
Talanta ; 223(Pt 2): 121872, 2021 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-33298292

RESUMEN

Metabolic phenotyping using mass spectrometry (MS) is being applied to ever increasing sample numbers in clinical and epidemiology studies. High-throughput and robust methods are being developed for the accurate measurement of metabolites associated with disease. Traditionally, quantitative assays have utilized triple quadrupole (QQQ) MS based methods; however, the use of such focused methods removes the ability to perform discovery-based metabolic phenotyping. An integrated workflow for the hybrid simultaneous quantification of 34 biogenic amines in combination with full scan high-resolution accurate mass (HRAM) exploratory metabolic phenotyping is presented. Primary and secondary amines are derivatized with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate prior to revered-phase liquid chromatographic separation and mass spectrometric detection. Using the HRAM-MS data, retrospective phenotypic data mining could be performed, demonstrating the versatility of HRAM-MS instrumentation in a clinical and molecular epidemiological environment. Quantitative performance was assessed using two MS detector platforms: Waters TQ-XS (QQQ; n = 3) and Bruker Impact II QToF (HRAMS-MS; n = 2) and three human biofluids (plasma, serum and urine). Finally, each platform was assessed using a certified external reference sample (NIST SRM 1950 plasma). Intra- and inter-day accuracy and precision were comparable between the QQQ and QToF instruments (<15%), with excellent linearity (R2 > 0.99) over the quantification range of 1-400 µmol L-1. Quantitative values were comparable across all instruments for human plasma, serum and urine samples, and calculated concentrations were verified against certified reference values for NIST SRM 1950 plasma as an external reference. As a real-life biological exemplar, the method was applied to plasma samples obtained from SARS-CoV-2 positive patients versus healthy controls. Both the QQQ and QToF approaches were equivalent in being able to correctly classify SARS-CoV-2 positivity. Critically, the use of HRAM full scan data was also assessed for retrospective exploratory mining of data to extract additional biogenic amines of biomarker interest beyond the 34 quantified targets.


Asunto(s)
Aminoácidos/metabolismo , Aminas Biogénicas/metabolismo , Aminoácidos/sangre , Aminas Biogénicas/sangre , /orina , Cromatografía Líquida de Alta Presión , Humanos , Espectrometría de Masas , Metabolómica , Fenotipo , Control de Calidad , Estándares de Referencia , Reproducibilidad de los Resultados , Estudios Retrospectivos
18.
Food Chem ; 334: 127475, 2021 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-32688176

RESUMEN

Although numerous types of organisms have been used to enrich selenium, a low-cost and efficient organism is yet to be identified. This study aimed to develop a new means of selenium enrichment using Tenebrio molitor larvae. Our results indicated that the total selenium content in larvae was increased 83-fold to 54.21 ± 1.25 µg/g, and of this content, organic selenium accounted for over 97% after feeding the larvae with 20 µg/g of sodium selenite. Selenium was distributed unequally in the protein fraction with following order: alkali-soluble protein-bound selenium (36.32%) > salt-soluble protein-bound selenium (19.41%) > water-soluble protein-bound selenium (17.03%) > alcohol-soluble protein-bound selenium (3.21%). Additionally, 81% of the selenium within the soluble proteins was distributed in subunits possessing molecular weights of <40 kDa. After hydrolysis by alcalase, the protein hydrolysate of selenium-enriched larvae possessing 75% selenium recovery exhibited stronger antioxidant and immunoregulatory activities than those of regular larvae.


Asunto(s)
Antioxidantes/farmacología , Factores Inmunológicos/farmacología , Proteínas de Insectos/metabolismo , Hidrolisados de Proteína/farmacología , Selenio/farmacocinética , Tenebrio/metabolismo , Adulto , Aminoácidos/análisis , Aminoácidos/metabolismo , Animales , Antioxidantes/metabolismo , Eritrocitos/efectos de los fármacos , Hemólisis/efectos de los fármacos , Humanos , Hidrólisis , Factores Inmunológicos/metabolismo , Proteínas de Insectos/farmacología , Larva/efectos de los fármacos , Larva/metabolismo , Ratones , Hidrolisados de Proteína/metabolismo , Células RAW 264.7 , Selenio/análisis , Subtilisinas/química , Subtilisinas/metabolismo , Tenebrio/efectos de los fármacos
19.
Food Chem ; 334: 127479, 2021 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-32688181

RESUMEN

Calcium treatment effects on malate metabolism and the GABA pathway in 'Cripps Pink' apple fruit during storage were investigated. Postharvest apple fruit treated with 1% and 4% calcium chloride solutions were stored at 25 ± 1 °C. The 4% calcium treatment suppressed declines in titratable acidity and malate content and increased succinate and oxalate concentrations. Calcium treatment also reduced the respiration rate and decreased ethylene production peak during storage. Moreover, 4% calcium treatment significantly enhanced cyNAD-MDH and PEPC activities and upregulated MdMDH1, MdMDH2, MdPEPC1 and MdPEPC2 expression while inhibiting cyNADP-ME and PEPCK activities and downregulating MdME1, MdME4 and MdPEPCK2 expression. Surprisingly, calcium treatment changed the content of some free amino acids (GABA, proline, alanine, aspartic acid and glutamate), two of which (glutamate and GABA) are primary metabolites of the GABA pathway. Furthermore, calcium application enhanced GABA pathway activity by increasing MdGAD1, MdGAD2, MdGABA-T1/2 and MdSSADH transcript levels.


Asunto(s)
Calcio/farmacología , Frutas/efectos de los fármacos , Malatos/metabolismo , Malus/efectos de los fármacos , Malus/metabolismo , Ácido gamma-Aminobutírico/metabolismo , Aminoácidos/análisis , Aminoácidos/metabolismo , Etilenos/metabolismo , Calidad de los Alimentos , Frutas/química , Frutas/genética , Frutas/metabolismo , Regulación de la Expresión Génica de las Plantas/efectos de los fármacos , Malus/química , Malus/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo
20.
Food Chem ; 334: 127517, 2021 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-32711266

RESUMEN

To facilitate selective breeding of polyphenol-rich peanuts, we looked for mass spectrometry-based proteomic evidence, investigating a subset of recombinant inbred lines (RILs) developed by the Australian peanut breeding program. To do this, we used label-free shotgun proteomics for protein and peptide quantitation, statistically analyzed normalized spectral abundance factors using R-package, as well as assayed important antioxidants. Results revealed statistically significant protein expression changes in 82 proteins classified between high or low polyphenols expressing RILs. Metabolic changes in polyphenol-rich RIL p27-362 point towards increased enzymatic breakdown of sugars and phenylalanine biosynthesis. The study revealed phenylpropanoid pathway overexpression resulting in increased polyphenols biosynthesis. Overexpression of antioxidant enzymes such as catalase, by 73.4 fold was also observed. A strong metabolic correlation exists with the observed phenotypic traits. Peanut RIL p27-362 presents a superior nutritional composition with antioxidant-rich peanut phenotype and could yield commercial profits. Data are available via ProteomeXchange with identifierPXD015493.


Asunto(s)
Arachis/metabolismo , Proteínas de Plantas/metabolismo , Polifenoles/química , Proteómica/métodos , Aminoácidos/metabolismo , Antioxidantes/química , Arachis/química , Biomarcadores/metabolismo , Cruzamiento , Catalasa/metabolismo , Cromatografía Líquida de Alta Presión , Fenotipo , Proteínas de Plantas/análisis , Polifenoles/aislamiento & purificación , Polifenoles/metabolismo , Extracción en Fase Sólida , Espectrometría de Masas en Tándem
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